So I think there are ways that you can do it to kill the flavor of books, but the core premise that some of those books are no longer appropriate for children as written is absolutely real. They're not capable of reading critically and recognizing that some of the characterizations aren't appropriate. They just absorb. And if you did want them to engage with "this isn't right", you need to be more direct with it and deliberately make it part of the story.
Adult books IDK. I'm not really a big classics reader generally, because while historical relevance is important, I just don't think a lot of the themes translate to modern culture. I'm kind of torn on reading them in literature class for the same reasons. They do provide examples of literary techniques that most modern stuff doesn't really do, so I can sort of understand using them to demonstrate allegory and metaphor, etc, but at the same time, very few people enjoy reading them and the actual messages that don't really apply today also don't get through anyways. If you read more modern stuff you might actually engage people with reading, but updating curriculums is a slog and a half.